PONE-D-24-56470Machine learning techniques for continuous genetic assignment of geographic origin of forest treesPLOS ONE

Dear Dr. Degen,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Mar 28 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Maher Maalouf, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2.  Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

3. Thank you for stating the following financial disclosure:

“BD & NM: Waldklimafonds WKF-22WC4111 01 & WKF-2219WK60A4 (German Federal Ministry of Food and Agriculture & German Federal German Ministry for the Environment, Nature Conservation and Nuclear Safety);  YY: No 23RL-1F017 from the Higher Education and Science Committee of the Republic of Armenia “

Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

If this statement is not correct you must amend it as needed.

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

4. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The article explores the application of machine learning regression techniques to identify the geographic origin of forest trees using genetic data. It evaluates five methods—Nearest Neighbor (NN), Gaussian Process Regression (GPR), Genomic Prediction (GP), and Deep Learning (DL)—across two datasets: one for European beech and another for pedunculate oak. The study concludes that grid-based GPR and DL demonstrate the highest accuracy, achieving errors below 8% for 90% of the samples. These methods have significant potential for tracking seed sources, detecting mislabeling, combating illegal logging, and enhancing forest management. The article is suitable for publication after minor revisions addressing the following points:

1. The authors should clarify the connection between terms like discrete and continuous assignments and machine learning concepts such as classification and regression.

2. The structure of the data matrix (X) must be clearly described for better understanding.

3. The quality of the figures needs improvement, ensuring the text on them is legible.

Reviewer #2: This is an interesting manuscript attempting to compare methods for assigning individuals within the species range based on individual genotypic data and know the distribution of genetic variants across latitudinal and longitudinal dimensions of the species. The manuscript tests several methods and implements them in two species: Fagus sylvatica and Quercus robur. The two species have different data sets for the number of individuals, the number and types of SNP markers, and the area and density of samples.

The manuscript seems technically sound, and the authors demonstrate good knowledge of the statistical parts of the study. The choice of several different and competing methods is a strong aspect of the paper.

I would expect a comment that the selection of the species beech and oak, both heavy-seeded with limited seed transfer capacity, could be beneficial for this study. Other species, such as conifers, e.g. Scots pine, would probably not allow for such efficient tracking of actual to predicted locations of individuals or groups due to a different spatial structure of genetic diversity.

I appreciate the comments that these methods might be of particular importance in the management of forest genetic resources and controlling the transfer of forest genetic material. However, I would also like to see the comments on how to design sampling data for possible future studies aimed at capturing spatial patterns of genetic diversity, which might be used to predict individual or group locations. In particular, I’m interested in the opinion of whether individual-based sampling or population sampling seems better for this type of research.

Overall, the manuscript is well written and has the potential to be influential for others interested in using genetic data to capture spatial patterns of genetic diversity distributions over larger geographic scales. I fully recommend this manuscript for publishing in PLOS-ONE; however, I provide some comments below, which might be helpful for further improvement of the manuscript.

Minor comments:

111, how many SNPs were nuclear vs. chloroplast? Chloroplast SNPs could be falsified due to the presence of chloroplast sequences in the nuclear genome (NUPTs –nuclear-encoded chloroplast DNA). How the chloroplast SNPs were verified? Based on coverage?

A comment about the usefulness of nuclear or chloroplast markers for spatial analyses is needed. Chloroplast markers are well known in oaks to be maternally inherited and

114, how was the admixture level determined?

127 ‘missing values’

132, how many were chloroplast vs nuclear SNPs ?

143, how were the nuclear and chloroplast SNPs used to obtain joint kinship matric? Uniparental and bi-parental markers have different implications for kinship construction. Were chloroplast SNPs threated as homozygous?

170, what is the rationale for 90:10 proportion of training and testing datasets?

TABLES, consider standardizing the order of methods. Now, the Table 1 has a different order of methods compared to other tables.

Table 3 and Table 4 are mentioned that they are for beech. It seems that Table 4 is for oak. ??

In my opinion, the figures 5-8 presenting outliers, should be presented in supplementary materials.

304, 10 group outliers out of how many? 99 groups?

321, 18 group outliers out of 188? (188 are mentioned earlier as locations, not as groups)

The citation format for references needs to conform to the journal standards.

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy .

Reviewer #1: No

Reviewer #2: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step.

Machine learning techniques for continuous genetic assignment of geographic origin of forest trees

PONE-D-24-56470R1

Dear Dr. Degen,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager®  and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Maher Maalouf, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The authors have thoroughly addressed my previous comments and incorporated the necessary modifications into the revised manuscript, resulting in a clearer and more comprehensive presentation of their work.

Reviewer #2: The Authors did a good job responding to all points and questions I raised in the former review report. In particular, I like the discussion of population vs. individual-based-sampling for assessing genetic diversity of the species, in particular important in the context of the topic of the manuscript. I believe, the manuscript reached the state ready for publication

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy .

Reviewer #1: No

Reviewer #2: No

**********